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Joel and Ellie head into the woods on the outskirts of the town of Lincoln. Ellie enjoys her first encounter with nature since she has never left the Boston Quarantine Zone before. They come up to an old water tower and work their way into the town, where Joel's friend Bill lives. They see a column of smoke in the distance and decide to head in that direction. Joel warns Ellie that Bill is a good guy, but is completely paranoid and dislikes strangers. They find that the town is filled with Bill's traps, barricades, and homemade bombs to keep the Infected from getting too close to his safehouses. They make their way through the back alleys until they reach a garage, where Joel is caught in one of Bill’s traps, resulting in him hanging upside down while Ellie attempts to cut him free as he shoots the Infected that rush in their direction. Just as Joel is about to be bitten, Bill shows up and leads them to an abandoned laundromat where they battle more infected before escaping into a bar.

As they rush into the bar, Bill is distrustful and angry at them for setting off his traps and attracting so many Infected to the area. He owes Joel a favor, who asks him for a car to get to his brother Tommy in Wyoming. Bill reluctantly agrees, but says that there are no functioning cars in town, only parts. They first must go to his other safehouse to gather weapons and supplies, because the parts are in a school filled with Infected. They reach his safehouse—a church—and gear up before heading out. Ellie wants a weapon as well, but Joel refuses. Bill says that, if they do this, then he owes Joel no more favors.

The three head out towards the graveyard, sneaking their way through an infestation of Clickers, and make their way through the rest of the Infected-filled town. They reach the school and kill the Runners surrounding it, before hiding from more Infected by climbing through a window near where the military truck crashed into the school.

A wave of Infected close in on them and they run into the school to escape, and after Bill realizes the car battery in the military truck is gone, he, Joel, and Ellie work their way through the school and run into a Bloater in the gym. They manage to kill it and escape into a nearby home. There, they find Bill’s old partner, Frank, who had committed suicide after being bitten so he wouldn't turn. They find a truck in the garage with Bill's battery in it, and if Joel searches the house, the Note from Frank can be found. Joel can give this note to Bill, who reads it, crumples it up and tosses it aside before the pair prepare to push the car down the nearby hill to start it. Ellie drives until Bill orders her to stop once they have escaped the infected. Bill then parts ways with Joel and Ellie, giving Joel a siphon hose to scavenge gasoline from abandoned cars. Before letting them leave, Bill confirms with Joel that they're square—no more favors to owe.

The Pills Note is on the floor at the far end of the room up the stairs and to the left, straight ahead of the broken fence you walk through and drop down.

The Note to Bob is in the barbed wire on the floor, past the camper van with Hui Wang 000197 on top of it.

The Perimeter Note is in the back room of the music shop, near the camper van.

The Note to Rachel is in the room with the infected in the house with the banging door, after finding the bow and crossing the roofs.

The Fences Note is in Bill's back room, near the pipe that he handcuffs Ellie to.

Bill's Map is on the table with the engine, near the door you come it through.

The Hunters Note, is on a table in the room to the rear and right of the stairs you come up after leaving Bill's safe room.

The Bombs Note is on a table in Bill's room (which is "not the confessional booth") in the church.

The Boy's Diary is on the windowsill upstairs in the room painted with stripes and cars, in the house with the dry pool outside.

The Note from Frank is in the house with Frank's body, in the room with the body next to the doorway.

After obtaining the Note from Frank, there is an optional conversation with Bill, where he will take the note, crumple it, and drop it on the floor. It can then be collected again, in a more crumpled state.

Hui Wang, 000197, is on top of the camper van that is across the street, just after the "Mandatory Evacuation Notice"

Alex Raymond Vincent, 000266, is suspended from a telephone pole in the area you fight the infected because Bill has "neglected the simple shit". It's exactly to the right from the door you enter the area by, and it requires a brick, bottle or bullet to get it down.

Peter Mrozik, 00)0263, is on top of a tumble drier in the first house you come to after Bill says it's "all new territory".

The moment when Joel steps on the snare trap, which results in him hanging upside down while being attacked by Runners and Clickers, is likely a nod to the 2007 movie I Am Legend. In said film, main character Robert Neville has the same thing happen to him, and almost gets killed by a group of Darkseekers as a result.